Which Orchard version is this? I'm not sure, but I think I heard something like this being fixed in 1.x. If you're not using 1.x, could you please give it a try and see if the issue is still there? If so, please file a bug. Thanks

If I remember correctly, this is precisely why the multiple index feature was implemented: you can build an "admin" index that also indexes draft contents. The way you do that is that once you have created the index, the content definition editor
for each content type lets you choose what versions get indexed: latest or published.